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Add --git-ssh option to installation #372

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merged 2 commits into from
Nov 24, 2017
Merged

Add --git-ssh option to installation #372

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1ecd2db
add --git-ssh option
sebastian-luna-valero Nov 24, 2017
83e1a4c
bugfix setup.py revert
sebastian-luna-valero Nov 24, 2017
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92 changes: 77 additions & 15 deletions install-CGAT-tools.sh
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Original file line number Diff line number Diff line change
Expand Up @@ -54,6 +54,16 @@ log() {
echo "# install-CGAT-tools.sh log | `hostname` | `date` | $1 "
}

# report error and exit
report_error() {
echo
echo $1
echo
echo "Aborting."
echo
exit 1
}

# detect CGAT installation
detect_cgat_installation() {

Expand Down Expand Up @@ -252,15 +262,21 @@ if [[ "$OS" != "travis" ]] ; then
# make sure you are in the CGAT_HOME folder
cd $CGAT_HOME

if [[ $INSTALL_ZIP ]] ; then
if [[ $CODE_DOWNLOAD_TYPE -eq 0 ]] ; then
# get the latest version from Git Hub in zip format
wget https://github.com/CGATOxford/CGATPipelines/archive/$PIPELINES_BRANCH.zip
unzip $PIPELINES_BRANCH.zip
rm $PIPELINES_BRANCH.zip
mv CGATPipelines-$PIPELINES_BRANCH/ cgat-pipelines/
else

elif [[ $CODE_DOWNLOAD_TYPE -eq 1 ]] ; then
# get latest version from Git Hub with git clone
git clone --branch=$PIPELINES_BRANCH https://github.com/CGATOxford/CGATPipelines.git $CGAT_HOME/cgat-pipelines
elif [[ $CODE_DOWNLOAD_TYPE -eq 2 ]] ; then
# get latest version from Git Hub with git clone
git clone --branch=$PIPELINES_BRANCH git@github.com:CGATOxford/CGATPipelines.git $CGAT_HOME/cgat-pipelines
else
report_error " Unknown download type for CGAT code... "
fi

# make sure you are in the CGAT_HOME/cgat-pipelines folder
Expand All @@ -280,9 +296,7 @@ if [[ "$OS" != "travis" ]] ; then
sed -i'' -e '/# dependencies/,/dependency_links=dependency_links,/d' setup.py
python setup.py develop

DEV_RESULT=$?

if [[ $DEV_RESULT -ne 0 ]] ; then
if [[ $? -ne 0 ]] ; then
echo
echo " There was a problem doing: 'python setup.py develop' "
echo " Installation did not finish properly. "
Expand All @@ -294,6 +308,10 @@ if [[ "$OS" != "travis" ]] ; then
print_env_vars

fi # if-$?

# revert setup.py if downloaded with git
[[ $CODE_DOWNLOAD_TYPE -ge 1 ]] && git checkout -- setup.py

fi # if INSTALL_DEVEL

# check whether conda create went fine
Expand Down Expand Up @@ -361,15 +379,20 @@ if [[ $JENKINS_INSTALL ]] ; then

else

if [[ $INSTALL_ZIP ]] ; then
if [[ $CODE_DOWNLOAD_TYPE -eq 0 ]] ; then
# get the latest version from Git Hub in zip format
wget https://github.com/CGATOxford/cgat/archive/$SCRIPTS_BRANCH.zip
unzip $SCRIPTS_BRANCH.zip
rm $SCRIPTS_BRANCH.zip
mv cgat-$SCRIPTS_BRANCH/ cgat-scripts/
else
elif [[ $CODE_DOWNLOAD_TYPE -eq 1 ]] ; then
# get latest version from Git Hub with git clone
git clone --branch=$SCRIPTS_BRANCH https://github.com/CGATOxford/cgat.git $CGAT_HOME/cgat-scripts
elif [[ $CODE_DOWNLOAD_TYPE -eq 2 ]] ; then
# get latest version from Git Hub with git clone
git clone --branch=$SCRIPTS_BRANCH git@github.com:CGATOxford/cgat.git $CGAT_HOME/cgat-scripts
else
report_error " Unknown download type for CGAT code... "
fi

cd cgat-scripts/
Expand All @@ -381,6 +404,21 @@ sed -i'' -e '/REPO_REQUIREMENT/,/pass/d' setup.py
sed -i'' -e '/# dependencies/,/dependency_links=dependency_links,/d' setup.py
python setup.py develop

if [[ $? -ne 0 ]] ; then
echo
echo " There was a problem doing: 'python setup.py develop' "
echo " Installation did not finish properly. "
echo
echo " Please submit this issue via Git Hub: "
echo " https://github.com/CGATOxford/CGATPipelines/issues "
echo
print_env_vars

fi # if-$?

# revert setup.py if downloaded with git
[[ $CODE_DOWNLOAD_TYPE -ge 1 ]] && git checkout -- setup.py

# go back to old working directory
cd $OLDWD

Expand Down Expand Up @@ -560,6 +598,21 @@ fi
}


# test whether --git-ssh download is doable
test_git_ssh() {
ssh-add -L >& /dev/null || SSH_KEYS_LOADED=$?
if [[ $SSH_KEYS_LOADED -ne 0 ]] ; then
echo
echo " Please load your ssh keys for GitHub before proceeding!"
echo
echo " Try: "
echo " 1. eval \$(ssh-agent)"
echo " 2. ssh-add ~/.ssh/id_rsa # or the file where your private key is"
report_error " and run this script again. "
fi
}


# function to display help message
help_message() {
echo
Expand Down Expand Up @@ -621,8 +674,11 @@ UNINSTALL=
UNINSTALL_DIR=
# where to install CGAT code
CGAT_HOME=
# instead of cloning with git, we can download zipped CGAT code
INSTALL_ZIP=1
# how to download CGAT code:
# 0 = as zip (default)
# 1 = git clone with https
# 2 = git clone with ssh
CODE_DOWNLOAD_TYPE=0
# which github branch to use (default: master)
PIPELINES_BRANCH="master"
SCRIPTS_BRANCH="master"
Expand Down Expand Up @@ -658,9 +714,20 @@ case $key in
shift # past argument
;;

--zip)
CODE_DOWNLOAD_TYPE=0
shift
;;

--git)
INSTALL_ZIP=
CODE_DOWNLOAD_TYPE=1
shift
;;

--git-ssh)
CODE_DOWNLOAD_TYPE=2
shift
test_git_ssh
;;

--production)
Expand Down Expand Up @@ -693,11 +760,6 @@ case $key in
shift 2
;;

--zip)
INSTALL_ZIP=1
shift
;;

--pipelines-branch)
PIPELINES_BRANCH="$2"
shift 2
Expand Down